I have used the pipeline and get the multiallelic sequences using the script get_multiseq.py.
However, I find some of the nodes of negative strands are not reverse complemented. This may be due to the codes in line 94-103 in script _getmultiseq.py:
if ind == (len(paths) - 1): try: totseq += grseq[path][:100] if chainstrand[2] == "+" else revcomp(grseq[path])[ :100] except: totseq += grseq[path] if chainstrand[2] == "+" else revcomp( grseq[path]) else: totseq += grseq[path] if chainstrand[2] == "+" else revcomp( grseq[path])
All of the chainstrand list are indexed as '2'. I think the index should be corrected as 'ind'.
Hi,
I have used the pipeline and get the multiallelic sequences using the script get_multiseq.py. However, I find some of the nodes of negative strands are not reverse complemented. This may be due to the codes in line 94-103 in script _getmultiseq.py:
if ind == (len(paths) - 1): try: totseq += grseq[path][:100] if chainstrand[2] == "+" else revcomp(grseq[path])[ :100] except: totseq += grseq[path] if chainstrand[2] == "+" else revcomp( grseq[path]) else: totseq += grseq[path] if chainstrand[2] == "+" else revcomp( grseq[path])All of the chainstrand list are indexed as '2'. I think the index should be corrected as 'ind'.
Please check about it.
Thanks for these useful tools!
Mian